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RosettaCM hybridize mover error after fragment picking

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RosettaCM hybridize mover error after fragment picking
#1

Hi all,

I am trying to do some comparitive modeling with RosettaCM by folowing the instructions here https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM

After fixing a few incorrect (apparently) hardcoded paths in the setup_RosettaCM.py, I can get the rosetta/main/source/bin/rosetta_scripts.static.linuxgccrelease application to run correctly all the way through the "BEGIN MOVER Hybridize - hybridize" and fragment picking steps. However, the program then quits after multiple errors as showin in the log fragment below...

A log of the full std out and std error is attached. 

If anyone can helpme fix this error I'd be most appreciative. 

Thanks.

-Andrew

protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Hybridize - hybridize=======================
core.fragment.picking_old.vall.vall_io: Reading Vall library from /home/ubuntu/rosetta/main/database//sampling/filtered.vall.dat.2006-05-05 ... 
core.fragment.picking_old.vall.vall_io:    100000
core.fragment.picking_old.vall.vall_io:    200000
core.fragment.picking_old.vall.vall_io:    300000
core.fragment.picking_old.vall.vall_io:    400000
core.fragment.picking_old.vall.vall_io:    500000
core.fragment.picking_old.vall.vall_io:    600000
core.fragment.picking_old.vall.vall_io:    700000
core.fragment.picking_old.vall.vall_io:    800000
core.fragment.picking_old.vall.vall_io:    900000
core.fragment.picking_old.vall.vall_io:    1000000
core.fragment.picking_old.vall.vall_io:    1100000
core.fragment.picking_old.vall.vall_io:    1200000
core.fragment.picking_old.vall.vall_io:    1300000
core.fragment.picking_old.vall.vall_io:    1400000
core.fragment.picking_old.vall.vall_io: ... done.  Read 1400124 lines.  Time elapsed: 8 seconds.
core.fragment.picking_old.vall.vall_io: Prior library contained 0 sections totaling 0 residues.
core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues.
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = NDHRYRRFT
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00059
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 5.00002
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = DHRYRRFTQ
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 4.00001
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 5.00003
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = HRYRRFTQL
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 4.00003
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00075
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RYRRFTQLP
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00079
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00047
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = YRRFTQLPN
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00019
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.0007
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RRFTQLPNG
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00038
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00033
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RFTQLPNGR
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00019
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00034
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = FTQLPNGRD
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00008
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00039
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = TQLPNGRDY
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00064
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.0004
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = QLPNGRDYH
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00024
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00058
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = LPNGRDYHY
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00086
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00068
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = PNGRDYHYS
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00016
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00054
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = NGRDYHYSV
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00001
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00067
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = GRDYHYSVV
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00059
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00044
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = RDYHYSVVG
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00058
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.0008
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = DYHYSVVGP
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 4
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00055
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = YHYSVVGPE
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00048
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00042
core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD  |  aa = HYSVVGPED
core.fragment.picking_old.vall.VallLibrarian: best fragment:   score = 3.00006
core.fragment.picking_old.vall.VallLibrarian: worst fragment:  score = 4.00043
protocols.hybridization.HybridizeProtocol: FRAGMENTS small max length: 3
protocols.hybridization.HybridizeProtocol: FRAGMENTS big max length: 9

ERROR: Assertion `weights_.size()` failed.
ERROR:: Exit from: src/numeric/random/WeightedSampler.cc line: 118
BACKTRACE:
[0x58c6188]
[0x574ee59]
[0x1131fdb]
[0x1132354]
[0x3544771]
[0x354593b]
[0x35460be]
[0x35aa058]
[0x35abb61]
[0x364e6d8]
[0x410acb]
[0x5e0bee4]
[0x6151fd]
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: 

File: src/numeric/random/WeightedSampler.cc:118
[ ERROR ] UtilityExitException
ERROR: Assertion `weights_.size()` failed.


protocols.jd2.JobDistributor: [ ERROR ] 

[ERROR] Exception caught by JobDistributor for job S_0001

File: src/numeric/random/WeightedSampler.cc:118
[ ERROR ] UtilityExitException
ERROR: Assertion `weights_.size()` failed.


protocols.jd2.JobDistributor: [ ERROR ] 
protocols.jd2.JobDistributor: [ WARNING ] S_0001 reported failure and will NOT retry
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER Hybridize - hybridize=======================
protocols.hybridization.HybridizeProtocol: FRAGMENTS small max length: 3
protocols.hybridization.HybridizeProtocol: FRAGMENTS big max length: 9

ERROR: Assertion `weights_.size()` failed.
ERROR:: Exit from: src/numeric/random/WeightedSampler.cc line: 118
BACKTRACE:
[0x58c6188]
[0x574ee59]
[0x1131fdb]
[0x1132354]
[0x3544771]
[0x354593b]
[0x35460be]
[0x35aa058]
[0x35abb61]
[0x364e6d8]
[0x410acb]
[0x5e0bee4]
[0x6151fd]
protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: 

File: src/numeric/random/WeightedSampler.cc:118
[ ERROR ] UtilityExitException
ERROR: Assertion `weights_.size()` failed.


 

UPDATE:

The apparently same error occurs on a macOS install too. The error logs may be somewhat more informative and are attached. 

 

 

AttachmentSize
error.log35.97 KB
macOS.log70.7 KB
Post Situation: 
Thu, 2018-09-06 11:03
amorin